X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJabaParamStore.java;h=34b8a72da3568002ae63c873e513feda56d33423;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=0f7d6facf31e0582ba2ad9d14f9ff1da29d09f4b;hpb=85037c7f026acf289a22eaf0bd0d368351b5905e;p=jalview.git

diff --git a/src/jalview/ws/jws2/JabaParamStore.java b/src/jalview/ws/jws2/JabaParamStore.java
index 0f7d6fa..34b8a72 100644
--- a/src/jalview/ws/jws2/JabaParamStore.java
+++ b/src/jalview/ws/jws2/JabaParamStore.java
@@ -1,12 +1,41 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.jws2;
 
-import java.io.BufferedReader;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.dm.JabaOption;
+import jalview.ws.jws2.dm.JabaParameter;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParamManager;
+import jalview.ws.params.WsParamSetI;
+
 import java.io.IOException;
-import java.io.Reader;
-import java.io.Writer;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.StringTokenizer;
 
 import compbio.metadata.Argument;
 import compbio.metadata.Option;
@@ -15,14 +44,6 @@ import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
 
-import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
-import jalview.ws.jws2.dm.JabaOption;
-import jalview.ws.jws2.dm.JabaParameter;
-import jalview.ws.jws2.dm.JabaWsParamSet;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.ParamDatastoreI;
-import jalview.ws.params.WsParamSetI;
-
 public class JabaParamStore implements ParamDatastoreI
 {
 
@@ -36,56 +57,44 @@ public class JabaParamStore implements ParamDatastoreI
 
   public JabaParamStore(Jws2Instance service)
   {
-    this.service = service;
-    serviceOptions = service.getRunnerConfig();
-    // TODO: discover all the user's locally sored presets for this service and populate the hash table
-    // TODO: for JAL-632
+    this(service, null);
   }
 
-  /**
-   * store the given parameters in the user parameter set database.
-   * 
-   * @param storeSetName
-   *          - lastParmSet
-   * @param descr
-   *          - setDescr.getText()
-   * @param jobParams
-   *          - getJobParams()
-   */
-  private void _storeUserPreset(String storeSetName, String descr,
-          List<Argument> jobParams)
-  {
-    // this is a simple hash store.
-    editedParams.put(storeSetName, new JabaWsParamSet(storeSetName, descr,
-            JabaParamStore.getJwsArgsfromJaba(jobParams)));
-    // writeParam("Saving " + storeSetName + ": ", jobParams);
-  }
+  ParamManager manager;
 
-  private void writeParam(String nm, List<Argument> params)
+  public JabaParamStore(Jws2Instance service, ParamManager manager)
   {
-    for (Argument p : params)
+    this.service = service;
+    serviceOptions = service.getRunnerConfig();
+    this.manager = manager;
+    // discover all the user's locally stored presets for this service and
+    // populate the hash table
+    if (manager != null)
     {
-      System.out.println(nm + ":" + System.identityHashCode(p) + " Name: "
-              + p.getName() + " Value: " + p.getDefaultValue());
+      manager.registerParser(service.getUri(), this);
+      WsParamSetI[] prams = manager.getParameterSet(null, service.getUri(),
+              true, false);
+      if (prams != null)
+      {
+        for (WsParamSetI paramset : prams)
+        {
+          if (paramset instanceof JabaWsParamSet)
+          {
+            editedParams.put(paramset.getName(), (JabaWsParamSet) paramset);
+          }
+          else
+          {
+            System.err
+                    .println("Warning: Ignoring parameter set instance of type "
+                            + paramset.getClass()
+                            + " : Bound but not applicable for service at "
+                            + service.getUri());
+          }
+        }
+      }
     }
   }
 
-  private JabaWsParamSet _getUserPreset(String setName)
-  {
-    JabaWsParamSet pset = editedParams.get(setName);
-    return pset;
-  }
-
-  /**
-   * remove the given user preset from the preset stash
-   * 
-   * @param setName
-   */
-  private void _deleteUserPreset(String setName)
-  {
-    editedParams.remove(setName);
-  }
-
   @Override
   public List<WsParamSetI> getPresets()
   {
@@ -133,24 +142,56 @@ public class JabaParamStore implements ParamDatastoreI
 
   public static List<ArgumentI> getJwsArgsfromJaba(List jabargs)
   {
+    return getJwsArgsfromJaba(jabargs, true);
+  }
+
+  public static List<ArgumentI> getJwsArgsfromJaba(List jabargs,
+          boolean sortByOpt)
+  {
     List<ArgumentI> rgs = new ArrayList<ArgumentI>();
+    List<String> rgnames = new ArrayList<String>();
     for (Object rg : jabargs)
     {
-      ArgumentI narg = (rg instanceof Parameter) ? new JabaParameter(
-              (Parameter) rg) : (rg instanceof Option) ? new JabaOption(
-              (Option) rg) : null;
+      ArgumentI narg = null;
+      String nargstring = null;
+      if (rg instanceof Parameter)
+      {
+        narg = new JabaParameter((Parameter) rg);
+        nargstring = narg.getName(); // just sort by name for this
+      }
+      else if (rg instanceof Option)
+      {
+        narg = new JabaOption((Option) rg);
+        nargstring = (String) ((Option) rg).getOptionNames().get(0);
+      }
       if (narg == null)
       {
-        throw new Error(
-                "Implementation Error: Cannot handle Jaba parameter object "
-                        + rg.getClass());
+        throw new Error(MessageManager.formatMessage(
+                "error.implementation_error_cannot_handle_jaba_param",
+                new String[] { rg.getClass().toString() }));
       }
       else
       {
         rgs.add(narg);
+        rgnames.add(nargstring);
       }
     }
-    return rgs;
+    if (!sortByOpt)
+    {
+      return rgs;
+    }
+    ArgumentI[] rgssort = rgs.toArray(new ArgumentI[rgs.size()]);
+    String[] rgssorton = rgnames.toArray(new String[rgs.size()]);
+    jalview.util.QuickSort.sort(rgssorton, rgssort);
+    ArgumentI tmp1;
+    int i = 0;
+    while (rgssort.length - i > i)
+    {
+      tmp1 = rgssort[rgssort.length - i - 1];
+      rgssort[rgssort.length - i - 1] = rgssort[i];
+      rgssort[i++] = tmp1;
+    }
+    return Arrays.asList(rgssort);
   }
 
   public static List getJabafromJwsArgs(List<ArgumentI> jwsargs)
@@ -162,9 +203,9 @@ public class JabaParamStore implements ParamDatastoreI
               .getOption() : null;
       if (narg == null)
       {
-        throw new Error(
-                "Implementation Error: Cannot handle Jaba parameter object "
-                        + rg.getClass());
+        throw new Error(MessageManager.formatMessage(
+                "error.implementation_error_cannot_handle_jaba_param",
+                new String[] { rg.getClass().toString() }));
       }
       else
       {
@@ -192,55 +233,145 @@ public class JabaParamStore implements ParamDatastoreI
   {
     if (editedParams.containsKey(name))
     {
+      WsParamSetI parameterSet = editedParams.get(name);
       editedParams.remove(name);
+      if (manager != null)
+      {
+        manager.deleteParameterSet(parameterSet);
+      }
       return;
     }
     if (servicePresets.containsKey(name))
     {
       throw new Error(
-              "Implementation error: Attempt to delete a service preset!");
+              MessageManager
+                      .getString("error.implementation_error_attempt_to_delete_service_preset"));
     }
   }
 
-
   @Override
   public void storePreset(String presetName, String text,
           List<ArgumentI> jobParams)
   {
     JabaWsParamSet jps = new JabaWsParamSet(presetName, text, jobParams);
+    jps.setApplicableUrls(new String[] { service.getUri() });
     editedParams.put(jps.getName(), jps);
+    if (manager != null)
+    {
+      manager.storeParameterSet(jps);
+    }
   }
 
   @Override
-  public boolean readParamSet(WsParamSetI wsp,
-          Reader reader) throws IOException
+  public void updatePreset(String oldName, String presetName, String text,
+          List<ArgumentI> jobParams)
   {
-    if (!(wsp instanceof JabaWsParamSet))
+    JabaWsParamSet jps = (JabaWsParamSet) ((oldName != null) ? getPreset(oldName)
+            : getPreset(presetName));
+    if (jps == null)
+    {
+      throw new Error(
+              MessageManager
+                      .formatMessage(
+                              "error.implementation_error_cannot_locate_oldname_presetname",
+                              new String[] { oldName, presetName }));
+    }
+    jps.setName(presetName);
+    jps.setDescription(text);
+    jps.setArguments(jobParams);
+    jps.setApplicableUrls(new String[] { service.getUri() });
+    if (oldName != null && !oldName.equals(jps.getName()))
     {
-      throw new Error("Implementation error: JabaWsParamSets can only be handled by JabaParamStore");
+      editedParams.remove(oldName);
     }
-    List<String> lines=new ArrayList<String>();
-    String line;
-    BufferedReader br = new BufferedReader(reader);
-    while ((line=br.readLine())!=null)
+    editedParams.put(jps.getName(), jps);
+
+    if (manager != null)
     {
-      lines.add(line);
+      manager.storeParameterSet(jps);
     }
-    ((JabaWsParamSet) wsp).setjabaArguments(ParameterUtils.processParameters(lines, serviceOptions, " "));
-    return true;
+  }
+
+  /**
+   * create a new, empty parameter set for this service
+   * 
+   * @return
+   */
+  WsParamSetI newWsParamSet()
+  {
+    return new JabaWsParamSet();
+  };
+
+  private boolean involves(String[] urls)
+  {
+    boolean found = false;
+    for (String url : urls)
+    {
+      if (service.getServiceTypeURI().equals(url)
+              || service.getUri().equalsIgnoreCase(url))
+      {
+        found = true;
+        break;
+      }
+    }
+    return found;
   }
 
   @Override
-  public boolean writeParamSet(WsParamSetI wsp,
-          Writer writer) throws IOException
-  {
-            if (!(wsp instanceof JabaWsParamSet))
-            {
-              throw new Error("Implementation error: JabaWsParamSets can only be handled by JabaParamStore");
-            }
-            writer.write(ParameterUtils.writeParameterSet(((JabaWsParamSet)wsp).getjabaArguments(), " ")
-                    .toString());
-            return true;
+  public WsParamSetI parseServiceParameterFile(String name, String descr,
+          String[] urls, String parameterfile) throws IOException
+  {
+    if (!involves(urls))
+    {
+      throw new IOException(
+              MessageManager
+                      .getString("error.implementation_error_cannot_find_service_url_in_given_set"));
+
+    }
+    JabaWsParamSet wsp = new JabaWsParamSet();
+    wsp.setName(name);
+    wsp.setDescription(descr);
+    wsp.setApplicableUrls(urls.clone());
+
+    List<String> lines = new ArrayList<String>();
+    StringTokenizer st = new StringTokenizer(parameterfile, "\n");
+    while (st.hasMoreTokens())
+    {
+      lines.add(st.nextToken());
+    }
+    wsp.setjabaArguments(ParameterUtils.processParameters(lines,
+            serviceOptions, " "));
+    return wsp;
+  }
+
+  @Override
+  public String generateServiceParameterFile(WsParamSetI pset)
+          throws IOException
+  {
+    if (!involves(pset.getApplicableUrls()))
+    {
+      throw new IOException(
+              MessageManager
+                      .formatMessage(
+                              "error.implementation_error_cannot_find_service_url_in_given_set_param_store",
+                              new String[] { service.getUri() }));
+    }
+    if (!(pset instanceof JabaWsParamSet))
+    {
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_jabaws_param_set_only_handled_by"));
+    }
+
+    StringBuffer rslt = new StringBuffer();
+    for (String ln : ParameterUtils.writeParameterSet(
+            ((JabaWsParamSet) pset).getjabaArguments(), " "))
+    {
+      rslt.append(ln);
+      rslt.append("\n");
+    }
+    ;
+    return rslt.toString();
   }
 
 }